Innovative Biomolecular Techniques to Assess Foods Microbial Community Structure, Function, and Dynamics

A special issue of Foods (ISSN 2304-8158). This special issue belongs to the section "Food Microbiology".

Deadline for manuscript submissions: closed (15 October 2021) | Viewed by 7539

Special Issue Editors


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Guest Editor
Department of Comparative Biomedicine and Food Science, Università degli Studi di Padova, Padua, Italy
Interests: food safety; food microbiota; shelf-life of food products; food spoilage

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Guest Editor
Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
Interests: food microbiome; medical microbiology; evolutionary biology; food spoilage

Special Issue Information

Dear Colleagues, 

The composition of the microbiota, the dynamics of its modification, and interactions between microorganisms are fundamental for defining the safety and the quality of food products. Biomolecular techniques drastically increased in the last decades and improved in terms of efficiency, processivity, and applicability. The development and improvement of next-generation sequencing (NGS) platforms and their application to food microbiology allows deep microbial community definition directly on food samples, avoiding the culture methods and making it possible to identify unculturable microorganisms. Great efforts have been devoted to improving the microbiota definition; however, much remains to be done in terms of creating and improving bioinformatic tools able to manage huge amounts of data. The application of the most commonly applied metabarcoding, as well as more innovative metagenomics and metatranscriptomics, providing an exhaustive description of microbial communities and dynamics in food products, represents the main goal for the future. These will provide insights into the spoilage process, community structure of food products, shelf-life modifications, as well as investigating the effects of food additives in microbial communities of food.

Prof. Dr. Barbara Cardazzo
Dr. Nadia Andrea Andreani
Guest Editors

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Keywords

  • food microbiota
  • DNA metabarcoding
  • metagenomics
  • metatranscriptomics
  • bioinformatics

Published Papers (2 papers)

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Research

17 pages, 4614 KiB  
Article
Combining Culture-Dependent and Culture-Independent Methods: New Methodology Insight on the Vibrio Community of Ruditapes philippinarum
by Angela Zampieri, Massimiliano Babbucci, Lisa Carraro, Massimo Milan, Luca Fasolato and Barbara Cardazzo
Foods 2021, 10(6), 1271; https://doi.org/10.3390/foods10061271 - 03 Jun 2021
Cited by 10 | Viewed by 4005
Abstract
Vibrios represent a natural contaminant of seafood products. V. alginolyticus, V. cholerae, V. parahaemolyticus and V. vulnificus are the most hazardous species to human health. Given the worldwide consumption of mollusc products, reliable detection of Vibrio species is recommended to prevent [...] Read more.
Vibrios represent a natural contaminant of seafood products. V. alginolyticus, V. cholerae, V. parahaemolyticus and V. vulnificus are the most hazardous species to human health. Given the worldwide consumption of mollusc products, reliable detection of Vibrio species is recommended to prevent human vibriosis. In this study, culture-dependent and -independent methods were compared and integrated to implement knowledge of the Manila clam Vibrio community composition. Here, 16S and recA-pyrH metabarcoding were applied to compare the microbial communities of homogenate clam samples (culture-independent method) and their culture-derived samples plated on three different media (culture-dependent method). In addition, a subset of plated clam samples was investigated using shotgun metagenomics. Homogenate metabarcoding characterized the most abundant taxa (16S) and Vibrio species (recA-pyrH). Culture-dependent metabarcoding detected the cultivable taxa, including rare species. Moreover, marine agar medium was found to be a useful substrate for the recovery of several Vibrio species, including the main human pathogenic ones. The culture-dependent shotgun metagenomics detected all the main human pathogenic Vibrio species and a higher number of vibrios with respect to the recA-pyrH metabarcoding. The study revealed that integration of culture-dependent and culture-independent methods might be a valid approach for the characterization of Vibrio biodiversity. Full article
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21 pages, 1053 KiB  
Article
Austrian Raw-Milk Hard-Cheese Ripening Involves Successional Dynamics of Non-Inoculated Bacteria and Fungi
by Narciso M. Quijada, Stephan Schmitz-Esser, Benjamin Zwirzitz, Christian Guse, Cameron R. Strachan, Martin Wagner, Stefanie U. Wetzels, Evelyne Selberherr and Monika Dzieciol
Foods 2020, 9(12), 1851; https://doi.org/10.3390/foods9121851 - 11 Dec 2020
Cited by 11 | Viewed by 2892
Abstract
Cheese ripening involves successional changes of the rind microbial composition that harbors a key role on the quality and safety of the final products. In this study, we analyzed the evolution of the rind microbiota (bacteria and fungi) throughout the ripening of Austrian [...] Read more.
Cheese ripening involves successional changes of the rind microbial composition that harbors a key role on the quality and safety of the final products. In this study, we analyzed the evolution of the rind microbiota (bacteria and fungi) throughout the ripening of Austrian Vorarlberger Bergkäse (VB), an artisanal surface-ripened cheese, by using quantitative and qualitative approaches. The real-time quantitative PCR results revealed that bacteria were more abundant than fungi in VB rinds throughout ripening, although both kingdoms were abundant along the process. The qualitative investigation was performed by high-throughput gene-targeted (amplicon) sequencing. The results showed dynamic changes of the rind microbiota throughout ripening. In the fresh products, VB rinds were dominated by Staphylococcus equorum and Candida. At early ripening times (14–30 days) Psychrobacter and Debaryomyces flourished, although their high abundance was limited to these time points. At the latest ripening times (90–160 days), VB rinds were dominated by S. equorum, Brevibacterium, Corynebacterium, and Scopulariopsis. Strong correlations were shown for specific bacteria and fungi linked to specific ripening periods. This study deepens our understanding of VB ripening and highlights different bacteria and fungi associated to specific ripening periods which may influence the organoleptic properties of the final products. Full article
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